Microbiology Genetics

mistiffy · Oct 19, 2007

Here are some of my notes on the chapter over microbial genetics, hope it helps some!

* Genome - the entire genetic complement of an organism; includes its genes and nucleotide sequences

The Structure of Prokaryotic Genomes

* Contained in two structures

* Chromosomes

* Plasmids

Prokaryotic Chromosomes

* Main portion of DNA, along with associated proteins and RNA, are packaged in 1-2 chromosomes

* Typical chromosome - circular molecule of DNA in nucleoid

Plasmids

* Small, circular molecules of DNA that replicate independently

* Carry information required for their own replication, and often for one or more cellular traits

* Not essential for normal bacterial metabolism, growth, or reproduction

* Can confer survival advantages

* Many types of plasmids

* Fertility factors

* Resistance factors

* Bacteriocin factors

* Virulence plasmids

* Cryptic plasmids

The Structure of Eukaryotic Genomes

* Contained in two structures

* Nuclear DNA

* Extranuclear DNA

Eukaryotic Chromosomes

* Typically have more than one chromosome per cell

* Chromosomes are linear and sequestered within membrane-bound nucleus

Extranuclear DNA of Eukaryotes

* DNA of mitochondria and chloroplasts is circular and resembles chromosomes of prokaryotes

* Only codes for about 5% of RNA and proteins

* Nuclear DNA codes for 95% of RNA and proteins

* Some fungi and protozoa carry plasmids

DNA Replication

* An anabolic polymerization process that requires monomers and energy

* Triphosphate deoxyribonucleotides serve both functions

* Key to replication is complementary structure of the two strands

* Replication is semiconservative - new strands composed of one original strand and one daughter strand

Initial Processes in DNA Replication

* DNA polymerase binds to each strand and adds nucleotides to hydroxyl group at 3' end of nucleic acid

* Replicates DNA only 5' to 3'

* Because strands are antiparallel, new strands synthesized differently

* Leading strand synthesized continuously

* Lagging strand synthesized discontinuously

Other Characteristics of DNA Replication

* Bidirectional

* DNA is methylated; methylation plays role in variety of processes

* Control of genetic expression

* Initiation of DNA replication

* Protection against viral infection

* Repair of DNA

Gene Function

* Genotype - set of genes in the genome

* Phenotype - physical features and functional traits of organism

Transfer of Genetic Information

* Transcription - information in DNA is copied as RNA nucleotide sequences

* Translation - polypeptides synthesized from RNA nucleotide sequences

* Central dogma of genetics

* DNA transcribed to RNA

* RNA translated to form polypeptides

Events in Transcription

* Three types of RNA transcribed from DNA

* mRNA

* rRNA

* tRNA

* Where occurs

* Nucleoid of prokaryotes

* Nucleus, mitochondria, and chloroplasts of eukaryotes

* Three steps

* Initiation

* Elongation

* Termination

RNA Polymerase Versus DNA Polymerase

* RNA polymerase does not require helicase

* RNA polymerase slower than DNA polymerase

* Uracil incorporated instead of thymine

* RNA polymerase lacks proofreading function (more errors)

Stages of Translation

* Three stages

* Initiation

* Elongation

* Termination

* All stages require additional protein factors

* Initiation and elongation require energy (GTP)

Termination

* Release factors somehow recognize stop codons and modify ribosome to activate ribozymes which sever polypeptide from final tRNA

* Ribosome dissociates into subunits

Control of Transcription

* 75% of genes are expressed at all times

* Other genes are regulated so they are only transcribed and translated when cell needs them

* Allows cell to conserve energy

* Regulation of protein synthesis

* Typically halt transcription

* Can stop translation directly

Operons

* Inducible operons - must be activated by inducers

* Lactose Operon

* Repressible operons - transcribed continually until deactivated by repressors

* Tryptophan Operon

Mutations of Genes

* Mutation - change in the nucleotide base sequence of a genome; rare

* Almost always deleterious

* Rarely lead to a protein having a novel property that improves ability of organism and its descendents to survive and reproduce

* Types

* Point mutations (most common) - one or a few base pairs affected

* Substitutions, insertions, and deletions

* Frameshift mutations - nucleotide triplets after the mutation displaced

* Insertions and deletions

Mutagens

* Radiation

* Ionizing radiation - induces breaks in chromosomes

* Nonionizing radiation - induces thymine dimers

* Chemical Mutagens

* Nucleotide analogs - disrupt DNA and RNA replication and cause point mutations

* Nucleotide-altering chemicals - result in base-pair substitution mutations and missense mutations

* Frameshift mutagens - result in nonsense mutations

Identifying Mutants, Mutagens, and Carcinogens

* Mutants - descendents of cell that does not successfully repair a mutation

* Wild types - cells normally found in nature

* Methods to recognize mutants

* Positive selection

* Negative (indirect) selection

* Ames test

Genetic Recombination and Transfer

* Exchange of DNA segments composed of homologous sequences

* Recombinants - cells with DNA molecules that contain new nucleotide sequences

* Vertical gene transfer - organisms replicate their genomes and provide copies to descendants

* Horizontal gene transfer - donor contributes part of genome to recipient; three types

* Transformation

* Transduction

* Bacterial Conjugation

Transformation

* Transforming agent was DNA; one of conclusive pieces of proof that DNA is genetic material

* Cells that take up DNA are competent; results from alterations in cell wall and cytoplasmic membrane that allow DNA to enter cell

Transduction

* Generalized transduction - transducing phage carries random DNA segment from donor to recipient

* Specialized transduction - only certain donor DNA sequences are transferred

Transposons and Transposition

* Segments of DNA that move from one location to another in the same or different molecule

* Result is a kind of frameshift insertion

* Transposons all contain palindromic sequences at each end

* Simplest transposons are insertion sequences which have no more than two inverted repeats and gene for transposase

* Complex transposons contain one or more genes not connected with transposition (e.g. antibiotic resistance)

emileth · Oct 20, 2007

Chapter 9 Genetics:

what is difference between eukaryotic and prokaryotic chromosome?

Eucaryotes chromosomes consist of a DNA molecule tightly wound around histone proteins, whereas a prokaryotic chromosome is condensed and secured into a packet by means of histone-like proteins. (Histone proteins help to hold the shape of the chromosome).

Eucaryotic chromosomes are located in the nuclues, vary in number for a few to hundreds; they can occur in pairs (diploid) or singles (haploid) and they appear elongate. Thechromosomes can contain thousands to hundreds of thousands genes.

Prokaryotic have a single cicular chromosome, which contain a few thousand genes.

How is DNA replicated?

DNA replication happens during the process of normal cell division cycles.DNA copies itself just before cellular division in theprocess of semisconservative replication. DNA replication requires a careful orchestration of the actions of 30 different enzymes which seperate the strands of the existing DNA molecule, copy its template and

produce two complete daughter molecules. Steps:

1) Uncoiling the parent DNA molecule

2) Unzipping the hydrogen bonds between the base pairs, thus seperating the two strands and exposing the nucleotide sequence of each strand to serve as templates

3) Synthesizing two new strands by attachment of the correct complemnetary nucleotide to each single stranded template.

What does semiconservative mean?

semiconservative means that each "parent" or "original" DNA molecule is preserved and used as a template.

why is the codon Amino Acid code considered to be degenerative?

The Condon Amino Acid code is considered to be degenerative because a particular amino acid can be coded for by more than one codon. It is important because it eliminates substitution problems.

What major enzymes are involved in DNA replication and what is their function (see table 9.1)?

Helicase- Unzipping the DNA helix

Primase- Synthesizing an RNA primer (meaning, START here)

DNA polymerase 3-Synthesizes the new daughter strand of DNA using the parental template. It adds bases to the new DNA chain; proofreading the chain for mistakes

DNA polymerease 1- Removing primer, closing gaps, repairing mismatches

Ligase- puts it back together again;

Gyrase- Recoiling

**Important. DNA polymerase 3 can only add nucleotides in one direction, so a new starnd is always synthesized 5 to 3.

Why are there multiple enzymes involved in DNA replication?

Enzymes are specific in their job and their a multiple steps in DNA replication that have to occur.

What is DNA composed of and what does DNA look like (sructure-wise)?

The base of DNA is a neocleotide. Each neucleotide is made up of

1) Nitrogen bases ( Purine and Pyrimidine) that pair up and attached by hydrogen bonds..

The Purines are adenine and guanine. The Pyramidines are thymine and cytosine. A always pairs with T and G always pairs with C.

2)Phosphate

3) Deoxribose sugar

It is a gigantic molecule with two strands combined into a double helix.

what is the general flow of genetics with an organism? (how do you get from DNA to protein?)

DNA->RNA->Protein

Information in DNA is converted to proteins by the process of transcription and translation.

what is transcription?

Transcription is the formation of RNA using DNA as a template.

what is translation?

Translation is the synthesis of proteins using RNA as a template.

what is an intron, where is it found?

An intron is the segements on split genes of eukaryotes that do not code for polypeptides. They can have regulatory functions.. They are found in the Pre-mRNA. The processing of pre-mRNA into mRNA involves the removal of introns.

What are the major kinds of RNA and what is their function?

Messenger RNA mRNA- carries the DNA master code to the ribisome so it can be translated.

Transfer RNA tRNA- brings amino acids to ribosome during translation.

Ribosomal rNA- forms the major part of a ribosome and participates in protein synthesis.

How is the DNA interpreted and a protein synthesized?

Step 1: DNA transcription (happens in the nucleus of eukaryotes)

A single strand of RNA is transcribed from a template strand of DNA. The result is mRNA, which is the copy of the structural gene or genes of DNA. In it, T is replaced by uracil. The message contain codon for a specific amino acid. mRNA is single stranded. After transcription, the mRNA is transported out of the cell's nucleus through nuclear pores to go to the site of translation, (the rough endoplasmic reticulum in eurkaryotes)

Step 2: RNA translation-

Ribosomes bind at the 5´-beginning of the mRNA and start scanning the mRNA for a Start-codon (AUG), a place where the protein synthesis starts.

The tRN anticodon with the correct attached amino acid binds to the start codon. Ribosomes move the next codon, allowing a new tRNA to bind and add another amino acid. These series of amino acids form peptide bonds. A stop condon terminates translation and there you have your protein!

In general, describe 2 mechanisms of regulation

Repressible- being made all the time unless you tell it to stop (ex: amino acids and nucleotides)

Inducable- not there until you tell it to make it. (ex: insulin)

what are the 3 categories of genes and what do they do? (structural, regulatory, encode RNA)

Structural- let's make a protein

Regulatory- control gen expression (make it or no, dont make it)

Encode for RNA- genes that code for RNA

what is a mutation? how are caused? are they good? bad? lethal?

A mutation is any change made to the DNA. It can be good or Bad. Sometimes it is lethal, but sometimes not. There are positive effects for the cell which allow the cell to adapt. There are also negative effects for the cells, which can result in lose of function or death of the cell.

Can you name a few things that result in mutation? (spontaneous, induced by mutagens)

Spontanous- Random Change as a result of a mistake made in copying of DNA. Happens at a known rate of about in a million.

Induced- caused by chemicals or radiation- examples are Agent Orange

Nonsense- a change in a normal codon into a stop condon, therefore you get incomplete proteins. Very common.

Frameshift- reading frame of the mRNA changes. If you knock out a base..

Back-mutation- mutation is reversed.

Can you name a few mutagens and what they do? (see table 9.3)

Acridine dyes- cause frameshifts due to insertion between base pairs

X rays- form free radicals that cause breaks in DNA

Ultaviolet radiation- causes cross links between adjacent pyrimidines

what is bacterial conjugation and what does it accomplish?

Bacterial conjugation is a type of recombination (sex for bacteria) where a plasmid (or other genetic material) is transferred by a dontor a receipiant via d direction connection. (via a pilus of donor cell that connects to a reciepient cell)

what is transformation?

nonspecific acceptance of free DNA (left around DNA)

what is transduction?

Donor is dead bacteria. Live recipient cell of same species. Bacteriophage infects host cells serve as the carrier of DNA from a dontor cell to a reciepent cell.